lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: Release (3.20)
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin
Maintainer: Lei Huang <lhuang1998 at gmail.com>
citation("lumi")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lumi")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.58.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (17.5 years) |
| License | LGPL (>= 2) |
| Depends | R (>= 2.10), Biobase(>= 2.5.5) |
| Imports | affy(>= 1.23.4), methylumi(>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods |
| System Requirements | |
| URL |
See More
| Suggests | beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | iCheck, wateRmelon, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, ffpeExampleData, lumiBarnes, MAQCsubset, mvoutData |
| Imports Me | arrayMvout, ffpe, MineICA |
| Suggests Me | beadarray, blima, Harman, methylumi, tigre, maGUI |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lumi_2.58.0.tar.gz |
| Windows Binary (x86_64) | lumi_2.58.0.zip |
| macOS Binary (x86_64) | lumi_2.58.0.tgz |
| macOS Binary (arm64) | lumi_2.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lumi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lumi |
| Bioc Package Browser | https://code.bioconductor.org/browse/lumi/ |
| Package Short Url | https://bioconductor.org/packages/lumi/ |
| Package Downloads Report | Download Stats |